Bengt Karlson

Environmental DNA (eDNA)-based detection has become an attractive method for determining biodiversity as it can provide more detailed information compared to traditional morphology-based approaches. This is especially relevant for targeting overall biodiversity or screening for the presence of harmful algal bloom (HAB) species. However, despite the availability of several general guidelines, the workflow for marine environments has yet to be standardised. This lack of standardisation complicates the comparison between samples across different monitoring programmes and projects. This project focused on the first step of the workflow – determining and standardising the minimum reliable sample volume needed to detect phytoplankton diversity under various environmental and biological conditions. A study and a workshop were conducted to test different sample volumes (1000 mL, 500 mL, 200 mL, and 20 mL), using samples collected from the Baltic and North Seas and northwestern Atlantic Ocean under various environmental conditions. Across the studied samples, 200 mL was identified as a sufficient sample volume to detect various species across the different volumes tested. This result represents an important first step towards standardising the eDNA-based approach and incorporating it into routine monitoring. Furthermore, the results of this project are expected to contribute to reducing the time and resources required for monitoring.

Phytoplankton constitute the base of the marine food web and is used all over theworld to assess the quality status of marine and freshwater systems. Phytoplanktonare for example used in the EU Marine Strategy Framework Directive and in theEU Water Framework Directive. There are long time series of data from monitoringprograms, where phytoplankton are analyzed using microscopy. However, presentlyDNA methods are quickly emerging. The aim of this project was to develop a practical and robust method to analyze phytoplankton that can be implemented inSwedish marine monitoring programs.The project was performed by joining the regular marine monitoring cruisesfor a period of one year (2019–2020). We collected parallel seawater samples forDNA metabarcoding of phytoplankton. Nineteen stations were sampled, all theway from the Bothnian Bay in the northern Baltic Sea to the Skagerrak adjacent tothe North Sea, with a sampling frequency of ~1 sampling per month. Best practiceswere developed for field sampling, DNA extraction, sequencing, bioinformatics andtaxonomic annotation. We also produced a system for data handling at the nationalhost, and provided a new data type for national data host for marine biology andoceanography, the National Oceanographic Data Centre (https://sharkweb.smhi.se/hamta-data/).An important part of the project was to compare results from DNA metabarcoding and microscopy. In general, results of DNA metabarcoding gives about twiceas high biodiversity measures than microscopy, even though it varies betweendifferent phytoplankton groups. We found that the reference databases have shortcomings and need to be further developed. To find out if DNA metabarcoding canbe used quantitatively, we added an internal standard to the samples, composedof synthetic DNA strings. The analysis showed varying results, and therefore furtherdevelopment is needed. The distribution of common eukaryotic groups showedrelatively good agreement between DNA metabarcoding and the carbon biomassmicroscopy metric, while biovolume and abundance showed larger deviations.With DNA metabarcoding we were able to produce detailed maps of the occurrenceof potentially harmful algae, for example the genus Prymnesium.By using physicochemical data measured in the monitoring programs wehave looked for environmental drivers of phytoplankton diversity and communitycomposition. Both salinity and nutrients were shown to have significant impactson the phytoplankton communities.In summary, we think that the developed DNA metabarcoding method wouldbe a valuable complement to the established microscopy-based phytoplanktonmonitoring.